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- PDB-2mxu: 42-Residue Beta Amyloid Fibril -

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Basic information

Entry
Database: PDB / ID: 2mxu
Title42-Residue Beta Amyloid Fibril
ComponentsAmyloid beta A4 protein
KeywordsPROTEIN FIBRIL / Amyloid Fibril / Amyloid beta
Function / homology
Function and homology information


amyloid-beta complex / negative regulation of presynapse assembly / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / regulation of Wnt signaling pathway / synaptic assembly at neuromuscular junction / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport ...amyloid-beta complex / negative regulation of presynapse assembly / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / regulation of Wnt signaling pathway / synaptic assembly at neuromuscular junction / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / axon midline choice point recognition / smooth endoplasmic reticulum calcium ion homeostasis / astrocyte activation involved in immune response / NMDA selective glutamate receptor signaling pathway / mating behavior / regulation of spontaneous synaptic transmission / ciliary rootlet / Golgi-associated vesicle / PTB domain binding / Lysosome Vesicle Biogenesis / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / positive regulation of amyloid fibril formation / neuron remodeling / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / nuclear envelope lumen / COPII-coated ER to Golgi transport vesicle / suckling behavior / signaling receptor activator activity / dendrite development / modulation of excitatory postsynaptic potential / TRAF6 mediated NF-kB activation / presynaptic active zone / positive regulation of protein metabolic process / neuromuscular process controlling balance / Advanced glycosylation endproduct receptor signaling / The NLRP3 inflammasome / negative regulation of long-term synaptic potentiation / regulation of multicellular organism growth / regulation of presynapse assembly / transition metal ion binding / intracellular copper ion homeostasis / negative regulation of neuron differentiation / ECM proteoglycans / spindle midzone / positive regulation of T cell migration / smooth endoplasmic reticulum / Purinergic signaling in leishmaniasis infection / forebrain development / positive regulation of chemokine production / clathrin-coated pit / Notch signaling pathway / protein serine/threonine kinase binding / positive regulation of G2/M transition of mitotic cell cycle / extracellular matrix organization / neuron projection maintenance / Mitochondrial protein degradation / response to interleukin-1 / positive regulation of mitotic cell cycle / ionotropic glutamate receptor signaling pathway / cholesterol metabolic process / positive regulation of calcium-mediated signaling / axonogenesis / dendritic shaft / platelet alpha granule lumen / adult locomotory behavior / positive regulation of glycolytic process / central nervous system development / learning / positive regulation of interleukin-1 beta production / trans-Golgi network membrane / positive regulation of long-term synaptic potentiation / endosome lumen / locomotory behavior / astrocyte activation / Post-translational protein phosphorylation / positive regulation of JNK cascade / microglial cell activation / regulation of long-term neuronal synaptic plasticity / serine-type endopeptidase inhibitor activity / synapse organization / TAK1-dependent IKK and NF-kappa-B activation / positive regulation of non-canonical NF-kappaB signal transduction / neuromuscular junction / visual learning / recycling endosome / positive regulation of interleukin-6 production / Golgi lumen / cognition / neuron cellular homeostasis / positive regulation of inflammatory response / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / endocytosis / cellular response to amyloid-beta / neuron projection development / G2/M transition of mitotic cell cycle / positive regulation of tumor necrosis factor production / apical part of cell / synaptic vesicle / cell-cell junction / Platelet degranulation
Similarity search - Function
Amyloidogenic glycoprotein, copper-binding / Amyloidogenic glycoprotein, copper-binding domain conserved site / Amyloidogenic glycoprotein, copper-binding domain superfamily / Copper-binding of amyloid precursor, CuBD / Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide / Beta-amyloid precursor protein C-terminal / Amyloidogenic glycoprotein, intracellular domain, conserved site ...Amyloidogenic glycoprotein, copper-binding / Amyloidogenic glycoprotein, copper-binding domain conserved site / Amyloidogenic glycoprotein, copper-binding domain superfamily / Copper-binding of amyloid precursor, CuBD / Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide / Beta-amyloid precursor protein C-terminal / Amyloidogenic glycoprotein, intracellular domain, conserved site / Beta-amyloid precursor protein C-terminus / Amyloid precursor protein (APP) intracellular domain signature. / Amyloidogenic glycoprotein, extracellular / Amyloidogenic glycoprotein, heparin-binding / Amyloidogenic glycoprotein, E2 domain / E2 domain superfamily / Amyloidogenic glycoprotein, heparin-binding domain superfamily / Amyloid A4 N-terminal heparin-binding / E2 domain of amyloid precursor protein / Amyloid precursor protein (APP) E1 domain profile. / Amyloid precursor protein (APP) E2 domain profile. / amyloid A4 / Amyloidogenic glycoprotein / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / PH-like domain superfamily
Similarity search - Domain/homology
Amyloid-beta precursor protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLID-STATE NMR / torsion angle dynamics, simulated annealing
AuthorsXiao, Y. / Ma, B. / McElheny, D. / Parthasarathy, S. / Long, F. / Hoshi, M. / Nussinov, R. / Ishii, Y.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: A beta (1-42) fibril structure illuminates self-recognition and replication of amyloid in Alzheimer's disease.
Authors: Xiao, Y. / Ma, B. / McElheny, D. / Parthasarathy, S. / Long, F. / Hoshi, M. / Nussinov, R. / Ishii, Y.
History
DepositionJan 14, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1May 20, 2015Group: Database references
Revision 1.2Jun 17, 2015Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Amyloid beta A4 protein
B: Amyloid beta A4 protein
C: Amyloid beta A4 protein
D: Amyloid beta A4 protein
E: Amyloid beta A4 protein
F: Amyloid beta A4 protein
G: Amyloid beta A4 protein
H: Amyloid beta A4 protein
I: Amyloid beta A4 protein
J: Amyloid beta A4 protein
K: Amyloid beta A4 protein
L: Amyloid beta A4 protein


Theoretical massNumber of molelcules
Total (without water)54,24112
Polymers54,24112
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28770 Å2
ΔGint-128 kcal/mol
Surface area16340 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 1000structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide
Amyloid beta A4 protein


Mass: 4520.087 Da / Num. of mol.: 12 / Fragment: UNP residues 672-713 / Source method: obtained synthetically
Details: chemically synthesized with Fmoc protected 13C- and 15N-labeled amino acids at selected sites
Source: (synth.) Homo sapiens (human) / References: UniProt: P05067

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR / Details: Amyloid Beta 42 Structural Model
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 13C-13C DARR (50 ms)
1212D 13C-13C DARR (200 ms)
1312D 13C-15N correlation
1411D 13C-13C fpRFDR-CT
1511D 13C-15N REDOR

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Sample preparation

DetailsContents: 50 uM [U-100% 13C; U-100% 15N] AB42, 10 mM sodium phosphate, 100% H2O
Solvent system: 100% H2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 uMAB42-1[U-100% 13C; U-100% 15N]1
10 mMsodium phosphate-21
Sample conditionspH: 7.4 / Pressure: ambient / Temperature: 283 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE4001
Varian UnityPlusVarianUNITYPLUS4002

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Processing

NMR softwareName: Amber / Version: 12 / Classification: refinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
Details: CYANA WAS USED TO OBTAIN 100 BEST STRUCTURE FROM 1000 TOTAL, AMBER 12 WAS USED TO REFINE 100 CYANA STRUCTURES TO BEST 10 STRUCTURES REPRESENTED HERE. THREE ROUNDS OF ANNEALING WERE USED.
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 1000 / Conformers submitted total number: 10

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